Ah being an old SW junkie I'll make thee comments...
1. The clone troopers as seen in Ep 1-3 (evil razzlefrazzin GL)
did have independent minds of their own and sought to have
some individualistic character to themselves. My evidence?
Thrawn Trilogy and the other books containing sleeper cells
of clone troopers.
2. A lot of this would have to depend on what point of the Empire's
timeline you are picking as the point they would go up against the Covanent...
At one time, yes, they did have multiple SSD command ships as well as numerous
other defense platforms, 3 Dstars (creation ability), the other Sun Crusher-esque ships.
The Eye of Palpatine, and numerous smaller vessels, not to mention alien plagues meant
to wipe out entire races.
But - most of this was not ready all at once, it was built in secret over time. Plus you have to factor
in that the Rebel Alliance did break them apart with the simple loss of Palpatine. Then spent the next
10 years cleaning up the warlords and portions of the Imperial Remnant before the truce. The Galactic
Alliance did have a sizable navy at the start of the NJO, including new Calamari Cruisers that could
rival SSD's due to the upgrades (if I remember that right). They also had at minimum, 3 captured SSDs...
The Guardian, Lusankya, and one other - which I'm thinking was part of the Black Fleet or something.
Might have to check the technical commentaries at the Force.net and the Wiki...
3. As to ground forces, I'd be willing to say the Covenant would likely win on the ground in
hand to hand or because of their walker units. The hand to hand though you'd just end up with
more stormtroopers dead per 1 elite. However, what's the Empire known to do... much less the Sith
before them? Bombard a planet from space until it's no longer inhabitable... But to invade a planet, you have
to control the space around it - otherwise you will be slowly cut off from support and eliminated. The same goes
for supply routes/hyperspace routes and planetary trade/manufacturing.
But there's my EU ten cents worth on the matter...